HNRNPH2

heterogeneous nuclear ribonucleoprotein H2, the group of Heterogeneous nuclear ribonucleoproteins|RNA binding motif containing

Basic information

Region (hg38): X:101408221-101414133

Previous symbols: [ "HNRPH2" ]

Links

ENSG00000126945 ∙ NCBI:3188 ∙ OMIM:300610 ∙ HGNC:5042 ∙ Uniprot:P55795 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• intellectual disability, X-linked, syndromic, Bain type (Strong), mode of inheritance: XL

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Intellectual developmental disorder, X-linked, syndromic, Bain type	XL	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Musculoskeletal; Neurologic	27545675

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the HNRNPH2 gene.

• not provided (21 variants)
• Intellectual disability, X-linked, syndromic, Bain type (11 variants)
• Inborn genetic diseases (4 variants)
• Fabry disease (2 variants)
• Stereotypic movement disorder;Abnormal facial shape (1 variants)
• Neurodevelopmental disorder (1 variants)
• HNRNPH2-related condition (1 variants)
• Neurodevelopmental delay (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HNRNPH2 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				6	1	7
missense	3	2	9	2		16
nonsense		1				1
start loss						0
frameshift		1	1			2
inframe indel			1			1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1		1	2
Total	3	4	12	8	2

Variants in HNRNPH2

This is a list of pathogenic ClinVar variants found in the HNRNPH2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
X-101408476-G-C		Fabry disease	Uncertain significance (Jul 16, 2020)
X-101408672-C-G		Fabry disease	Benign (Jan 22, 2024)
X-101412003-G-A			Likely benign (Sep 01, 2022)
X-101412036-G-A		HNRNPH2-related disorder	Likely benign (Mar 08, 2019)
X-101412073-C-T		Intellectual disability, X-linked, syndromic, Bain type	Likely pathogenic (Dec 12, 2018)
X-101412126-C-A			Likely benign (Dec 20, 2018)
X-101412328-C-T		Intellectual disability, X-linked, syndromic, Bain type	Pathogenic (Jan 28, 2022)
X-101412444-AG-A		Intellectual disability, X-linked, syndromic, Bain type	Likely pathogenic (Oct 04, 2022)
X-101412452-C-G			Uncertain significance (Dec 09, 2019)
X-101412464-T-A			Uncertain significance (Oct 25, 2023)
X-101412559-GT-G			Uncertain significance (Sep 20, 2019)
X-101412592-A-C		Inborn genetic diseases	Uncertain significance (Apr 11, 2023)
X-101412601-C-T		Intellectual disability, X-linked, syndromic, Bain type	Likely pathogenic (Jul 08, 2022)
X-101412604-C-T		Intellectual disability, X-linked, syndromic, Bain type • Inborn genetic diseases • Neurodevelopmental disorder • Neurodevelopmental delay • Stereotypic movement disorder;Abnormal facial shape	Pathogenic/Likely pathogenic (Mar 01, 2024)
X-101412605-G-A		Intellectual disability, X-linked, syndromic, Bain type • HNRNPH2-related disorder	Pathogenic (Jan 11, 2024)
X-101412614-C-T		Intellectual disability, X-linked, syndromic, Bain type	Pathogenic (Mar 12, 2018)
X-101412617-A-G		Inborn genetic diseases • Intellectual disability, X-linked, syndromic, Bain type	Conflicting classifications of pathogenicity (Apr 17, 2018)
X-101412623-G-C		Intellectual disability, X-linked, syndromic, Bain type	Likely pathogenic (Apr 20, 2018)
X-101412624-G-T			Likely pathogenic (Apr 16, 2020)
X-101412626-C-T			Uncertain significance (Aug 14, 2023)
X-101412627-G-A			Likely benign (Feb 01, 2024)
X-101412650-G-T		Inborn genetic diseases	Uncertain significance (Dec 13, 2023)
X-101412697-G-A			Uncertain significance (Dec 06, 2021)
X-101412725-A-G		Intellectual disability, X-linked, syndromic, Bain type	Uncertain significance (Mar 24, 2020)
X-101412757-T-A		HNRNPH2-related disorder	Likely benign (Aug 31, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HNRNPH2	protein_coding	protein_coding	ENST00000316594	1	5839

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.954	0.0454	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.62	42	178	0.236	0.0000132	2975
Missense in Polyphen		3	42.507	0.070577		820
Synonymous	0.332	63	66.4	0.948	0.00000520	868
Loss of Function	2.89	0	9.69	0.00	8.81e-7	172

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: This protein is a component of the heterogeneous nuclear ribonucleoprotein (hnRNP) complexes which provide the substrate for the processing events that pre-mRNAs undergo before becoming functional, translatable mRNAs in the cytoplasm. Binds poly(RG).
• Pathway: mRNA Processing;Metabolism of RNA;mRNA Splicing - Major Pathway;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Recessive Scores

• pRec: 0.221

Intolerance Scores

• loftool: 0.111
• rvis_EVS: -0.14
• rvis_percentile_EVS: 42.88

Haploinsufficiency Scores

• pHI: 0.913
• hipred: Y
• hipred_score: 0.840
• ghis: 0.467

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.860

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Low	Medium
Primary Immunodeficiency	Medium	Low	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Hnrnph2

Gene ontology

• Biological process: mRNA splicing, via spliceosome;RNA metabolic process
• Cellular component: nucleus;nucleoplasm;cytosol;postsynaptic density;membrane;ribonucleoprotein complex
• Molecular function: RNA binding;protein binding